Variant report

Variant	rs11125568
Chromosome Location	chr2:55635505-55635506
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55629328..55632200-chr2:55634808..55637417,2	K562	blood:
2	chr2:55629189..55632200-chr2:55632234..55637417,4	K562	blood:
3	chr2:55633136..55639027-chr2:55639441..55643745,9	K562	blood:
4	chr2:55617949..55620712-chr2:55634436..55637353,2	K562	blood:

Extended variants
information (count: 93 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10169185	0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10184756	0.84[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10198652	0.83[CHB][hapmap]
rs11125569	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11125572	0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11695152	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12617891	0.83[CHB][hapmap]
rs12618795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13008631	0.83[AFR][1000 genomes]
rs1454415	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1454419	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1545554	0.83[CHB][hapmap]
rs1598163	0.83[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs1902056	0.88[CHB][hapmap]
rs1902057	0.89[CHB][hapmap]
rs1902061	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1902062	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2045132	0.89[CHB][hapmap]
rs2045134	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2045135	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045136	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2100454	0.86[ASN][1000 genomes]
rs2123983	0.85[JPT][hapmap]
rs2219130	0.90[AFR][1000 genomes]
rs2576688	0.89[CHB][hapmap]
rs2576703	0.84[CHB][hapmap]
rs2589057	0.89[CHB][hapmap]
rs2589068	0.89[CHB][hapmap]
rs2589069	0.89[CHB][hapmap]
rs2589070	0.84[CHB][hapmap]
rs2589078	0.89[CHB][hapmap]
rs28501559	0.84[ASN][1000 genomes]
rs2864831	0.84[CHB][hapmap]
rs2867178	0.82[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs2867179	0.94[AFR][1000 genomes]
rs2902857	0.84[CHB][hapmap]
rs2903509	0.84[CHB][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2917777	0.84[CHB][hapmap]
rs2920963	0.83[CHB][hapmap]
rs2920970	0.84[CHB][hapmap]
rs2966466	0.84[CHB][hapmap]
rs3099080	0.83[CHB][hapmap]
rs3099081	0.87[CHB][hapmap]
rs3099083	0.89[CHB][hapmap]
rs3748943	0.84[JPT][hapmap]
rs4233960	0.84[CHB][hapmap]
rs4233961	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4277563	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4352263	0.92[ASN][1000 genomes]
rs4481025	0.86[JPT][hapmap]
rs4672032	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs4672033	0.99[ASN][1000 genomes]
rs4672034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672035	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672036	0.86[JPT][hapmap]
rs4672037	0.86[JPT][hapmap]
rs4672038	0.86[JPT][hapmap]
rs4672040	0.85[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672043	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672044	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672045	0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56201519	0.88[AFR][1000 genomes]
rs56225989	0.87[ASN][1000 genomes]
rs58708869	0.88[AFR][1000 genomes]
rs6545489	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6545490	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6545491	0.86[JPT][hapmap]
rs6545492	0.81[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6705104	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6709204	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6710192	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs6720698	0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6721593	0.84[JPT][hapmap]
rs6724840	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6725968	0.84[CHB][hapmap]
rs6733814	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7424286	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7559987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574743	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7579037	0.86[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7586440	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7589279	0.89[CHB][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7595396	0.86[ASN][1000 genomes]
rs7601340	0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7601588	0.83[CHB][hapmap]
rs7602189	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7603105	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7606361	0.83[CHB][hapmap]
rs9751964	0.93[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55542400-55644800	Weak transcription	Primary T cells from cord blood	blood
2	chr2:55555200-55635800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:55579200-55640800	Weak transcription	Fetal Brain Male	brain
4	chr2:55579400-55644400	Weak transcription	Primary B cells from cord blood	blood
5	chr2:55589400-55639400	Weak transcription	Aorta	Aorta
6	chr2:55591000-55646000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:55592800-55635600	Weak transcription	HSMMtube	muscle
8	chr2:55601800-55644600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:55616800-55642600	Weak transcription	HUVEC	blood vessel
10	chr2:55618200-55639400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:55618200-55642400	Weak transcription	Fetal Lung	lung
12	chr2:55618600-55636000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr2:55619200-55636800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:55623000-55635600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:55623200-55644400	Weak transcription	Fetal Kidney	kidney
16	chr2:55624200-55635600	Weak transcription	NHEK	skin
17	chr2:55624400-55645600	Weak transcription	Ovary	ovary
18	chr2:55627800-55636000	Weak transcription	NHDF-Ad	bronchial
19	chr2:55628600-55646000	Weak transcription	Esophagus	oesophagus
20	chr2:55629000-55635600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr2:55629600-55636200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:55630400-55645800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:55630600-55644200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:55630800-55642400	Weak transcription	Pancreas	Pancrea
25	chr2:55630800-55644800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr2:55630800-55645200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:55630800-55645200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:55631000-55639000	Weak transcription	A549	lung
29	chr2:55631000-55645400	Weak transcription	Placenta	Placenta
30	chr2:55631200-55635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:55631200-55636400	Weak transcription	K562	blood
32	chr2:55631200-55638600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:55631200-55642600	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:55631400-55635800	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr2:55631400-55642600	Weak transcription	Right Ventricle	heart
36	chr2:55631600-55639200	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:55631800-55645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:55632000-55644800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:55632600-55645800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:55632800-55637200	Weak transcription	HepG2	liver
41	chr2:55632800-55639200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:55632800-55640000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:55632800-55645800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:55633000-55635600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:55633000-55635600	Weak transcription	Fetal Brain Female	brain
46	chr2:55633000-55635600	Weak transcription	GM12878-XiMat	blood
47	chr2:55633000-55639400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:55633000-55645000	Weak transcription	Liver	Liver
49	chr2:55633000-55645800	Weak transcription	Fetal Intestine Small	intestine
50	chr2:55633000-55645800	Weak transcription	Spleen	Spleen

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